Journal of Biogeography
SU P P ORT IN G I NF ORM A T I ON
Testing a time hypothesis in the biogeography of the
arowana genus Scleropages (Osteoglossidae)
Sébastien Lavoué
APPENDIX S1 Species list and GenBank sequences.
Table S1 Species list and corresponding GenBank accession numbers.
Text S1 Additional fossils used in all reconstructions to calibrate internal nodes.
APPENDIX S2 Nucleotide substitution saturation plots.
Figure S1 Nucleotide substitution saturation plots
APPENDIX S3 Time-calibrated phylogenetic trees using different fossil calibration
strategies.
Figure S2 Bayesian time-calibrated phylogenetic trees under the O72R251 fossil
calibration strategies.
Figure S3 Bayesian time-calibrated phylogenetic trees under the O113R199 fossil
calibration strategies.
Figure S4 Bayesian time-calibrated phylogenetic trees under the O72R199 fossil
calibration strategies.
Journal of Biogeography
Supporting Information
APPENDIX S1 Species list and GenBank sequences.
Table S1 Species list and corresponding GenBank accession numbers. The familial and subfamilial classification is from Lavoué &
Sullivan (2004). Osteoglossid taxa are highlighted in grey.
Classification
Species
Osteoglossomorpha
Osteoglossidae
Arapaiminae
Osteoglossinae
Notopteridae
Xenomystinae
Notopterinae
Mormyridae
Mormyrinae
Petrocephalinae
Gymnarchidae
Pantodontidae
Hiodontidae
Elopomorpha (outgroup)
Elopidae
S. Lavoué
Mitogenome accession number
Reference
Heterotis niloticus
Arapaima gigas
Scleropages formosus
Scleropages jardinii
Scleropages leichardti
Osteoglossum bicirrhosum
AP009498
AP009497
DQ023143
KF481952
FJ890319
AB043025
Lavoué et al. (2011)
Lavoué et al. (2011)
Yue et al. (2006)
Mu et al. (2015)
Q. Lin et al. (unpubl.)
Inoue et al. (2009)
Papyrocranus congoensis
Xenomystus nigri
Notopterus notopterus
Chitala ornata
AP008926
AP009503
AP008924
AP008923
Inoue et al. (2009)
Lavoué et al. (2011)
Inoue et al. (2009)
Inoue et al. (2009)
Myomyrus macrops
Gnathonemus petersii
Petrocephalus soudanensis
Petrocephalus microphthalmus
Gymnarchus niloticus
Pantodon buchholzi (Niger population)
Pantodon buchholzi (Congo population)
Hiodon alosoides
Hiodon tergisus
AP009501
AP009611
AP009502
AP009609
AP009610
AB043068
AP011564
AP004356
AP009499
Lavoué et al. (2011)
Lavoué et al. (2011)
Lavoué et al. (2011)
Lavoué et al. (2011)
Lavoué et al. (2011)
Inoue et al. (2009)
Lavoué et al. (2011)
Inoue et al. (2009)
Lavoué et al. (2011)
Elops hawaiensis
AB051070
Inoue et al. (2004)
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Supporting Information
REFERENCES
Inoue, J.G., Miya, M., Tsukamoto, K. & Nishida, M. (2004) Mitogenomic evidence for the
monophyly of elopomorph fishes (Teleostei) and the evolutionary origin of the leptocephalus larva. Molecular Phylogenetics and Evolution, 32, 274–286.
Inoue, J.G., Kumazawa, Y., Miya, M. & Nishida, M. (2009) The historical biogeography of
the freshwater knifefishes using mitogenomic approaches: a Mesozoic origin of the
Asian notopterids (Actinopterygii: Osteoglossomorpha). Molecular Phylogenetics and
Evolution, 51, 486–499.
Lavoué, S., Miya, M., Arnegard, M.E., McIntyre, P.B., Mamonekene, V. & Nishida, M.
(2011) Remarkable morphological stasis in an extant vertebrate despite tens of
millions of years of divergence. Proceedings of the Royal Society B: Biological Sciences,
278, 1003–1008.
Mu, X.-D., Yang, Y.-X., Liu, Y., Song, H.-M., Luo, J.-R. & Hu, Y.-C. (2015) Complete mitochondrial genome of northern spotted barramundi, Scleropages jardinii. Mitochondrial DNA. doi:10.3109/19401736.2013.843080.
Yue, G.H., Liew, W.C. & Orban, L. (2006) The complete mitochondrial genome of a basal
teleost, the Asian arowana (Scleropages formosus, Osteoglossidae). BMC Genomics, 7,
e242.
S. Lavoué
Biogeography of the Asian and Australian arowanas
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Journal of Biogeography
Supporting Information
Text S1 The three additional fossils used in all reconstructions to calibrate internal
nodes are: (1) †Yanbiania wangqingica, dated to the Barremian age (129.4–125.0 Ma)
(Zhang, 2004; Wilson & Murray, 2008) that is the oldest fossil unambiguously assigned
to the crown-group Osteoglossomorpha (Li & Wilson, 1996; Wilson & Murray, 2008).
†Yanbiania wangqingica calibrates the age of the crown-group Osteoglossomorpha to a
minimum of 125.0 Ma; (2) †Palaeonotopterus greenwoodi from the Cenomanian stage
(100.5–93.6 Ma) is considered to be the most ancient representative of the crown group
(Notopteridae, Mormyroidea) (Forey, 1997; Taverne, 2000; Cavin & Forey, 2001; Hilton,
2003). I used this fossil to provide a minimum age (93.6 Ma) for the most recent common ancestor (MRCA) of the clade (Notopteridae, Mormyroidea); and (3) the minimum
time divergence between Heterotis and Arapaima may be constrained to Late Palaeocene because of an undescribed basioccipital complex from Bolivia which is ‘decidedly
Arapaima-like’ (citation from Forey & Hilton, 2010). I used this fossil to constrain the
time of the MRCA of the crown-group Arapaiminae to a minimum of 61.6 Ma.
REFERENCES
Cavin, L. & Forey, P.L. (2001) Osteology and systematic affinities of Palaeonotopterus
greenwoodi Forey 1997 (Teleostei: Osteoglossomorpha). Zoological Journal of the
Linnean Society, 133, 25–52.
Forey, P.L. (1997) A Cretaceous notopterid (Pisces: Osteoglossomorpha) from Morocco.
South African Journal of Science, 93, 564–569.
Forey, P.L. & Hilton, E.J. (2010) Two new tertiary osteoglossid fishes (Teleostei: Osteoglossomorpha) with notes on the history of the family. Morphology, phylogeny and
paleobiogeography of fossil fishes (ed. by D.K. Elliott, J.G. Maisey, X. Yu and D. Miao),
pp. 215–246. Friedrich Pfeil, Munich, Germany.
Hilton, E.J. (2003) Comparative osteology and phylogenetic systematics of fossil and
living bony-tongue fishes (Actinopterygii, Teleostei, Osteoglossomorpha). Zoological
Journal of the Linnean Society, 137, 1–100.
Li, G.-Q. & Wilson, M.V.H. (1996) Phylogeny of Osteoglossomorpha. Interrelationships of
fishes (ed. by M.L.J. Stiassny, L.R. Parenti and G.D. Johnson), pp. 163–174. Academic
Press, New York.
Taverne, L. (2000) Nouvelles données ostéologiques et phylogénétiques sur Palaeonotopterus greenwoodi, notoptéridé (Teleostei, Osteoglossomorpha) du Cénomanien
inférieur continenetal (Crétacé) du Maroc. Stuttgarter Beiträge zur Naturkunde Serie
B (Geologie und Paläontologie), 293, 1–24.
Wilson, M.V.H. & Murray, A.M. (2008) Osteoglossomorpha: phylogeny, biogeography,
and fossil record and the significance of key African and Chinese fossil taxa. Geological Society, London, Special Publications, 295, 185–219.
Zhang, J.-Y. (2004) New fossil osteoglossomorph from Ningxia, China. Journal of Vertebrate Paleontology, 24, 515–524.
S. Lavoué
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Supporting Information
APPENDIX S2 Nucleotide substitution saturation plots.
Figure S1 Nucleotide substitution saturation plots: the proportion of transitions (black
dots) and transversions (open dots) were plotted against sequence divergence using
Jukes–Cantor evolutionary distance in the program DAMBE5. Dashed lines are correlation
line with regression coefficient (r2) indicated.
Second positions
First positions
0.14
0.06
0.12
r2 = 0.89
0.05
r2 = 0.90
0.10
0.04
0.08
0.03
0.06
0.02
0.04
0.02
r2 = 0.75
0.01
r2 = 0.87
0
0
0
0.05
0.1
0
0.25
0.2
0.15
0.04
0.02
0.06
0.08
Third positions
0.4
0.35
r2 = 0.36
0.3
0.25
r2 = 0.33
0.2
0.15
0.1
0.05
0
0
tRNAs
0.18
2
12S and 16S rRNAs
0.14
0.16
r2 = 0.87
0.12
r2 = 0.95
0.14
1.5
1
0.5
0.1
0.12
0.08
0.1
r2 = 0.72
0.08
0.06
0.06
r2 = 0.86
0.04
0.04
0.02
0.02
0
0
0
S. Lavoué
0.1
0.2
0.3
0
0.1
0.2
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0.3
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Supporting Information
APPENDIX S3 Time-calibrated phylogenetic trees using different fossil calibration
strategies (O72R251, O113R199 and O72R199).
Figure S2 Bayesian time-calibrated phylogenetic trees under the O72R251 fossil calibration strategies using the complete matrix 1 (panel A) and the matrix 1 that excluded
saturated partitions (panel B). Phylogenetic informativeness profiles of each partition in
each matrix are shown above to the corresponding tree. In both trees, the age of the
root is constraint to a minimum of 251.2 Ma while the age of the crown group
Osteoglossidae is constraint to a minimum of 113 Ma. Calibration constraints follow
exponential distributions. Elops hawaiensis is used to root the trees. Horizontal timescale is in millions of years ago (Ma). 95% age credibility intervals are shown as black
horizontal bars (focal node of interest), and grey horizontal bars (all other nodes). All
posterior probability support values at nodes equal 1 except for the Scleropages node in
reconstruction B which is equal to 0.96. The effective age prior on the age of Scleropages
is shown in (c), for each time-tree reconstruction. Timing of possible freshwater route
between Sundaland and Australia–New Guinea predating the separation between India
and Antarctica–Australia is depicted by light orange background with a minimum at
115 Ma.
S. Lavoué
Biogeography of the Asian and Australian arowanas
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Journal of Biogeography
S. Lavoué
Supporting Information
Biogeography of the Asian and Australian arowanas
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Journal of Biogeography
Supporting Information
Figure S3 Bayesian time-calibrated phylogenetic trees under the O113R199 fossil
calibration strategies using the complete matrix 1 (panel A) and the matrix 1 that
excluded saturated partitions (panel B). Phylogenetic informativeness profiles of each
partition in each matrix are shown above to the corresponding tree. In both trees, the
age of the root is constraint to a minimum of 199.0 Ma while the age of the crown group
Osteoglossidae is constraint to a minimum of 113 Ma. Calibration constraints follow
exponential distributions. Elops hawaiensis is used to root the trees. Horizontal timescale is in millions of years ago (Ma). 95% age credibility intervals are shown as black
horizontal bars (focal node of interest), and grey horizontal bars (all other nodes). All
posterior probability support values at nodes equal 1 except for the Scleropages node in
reconstruction B which is equal to 0.96. The effective age prior on the age of Scleropages
is shown in (c), for each time-tree reconstruction. Timing of possible freshwater route
between Sundaland and Australia–New Guinea predating the separation between India
and Antarctica–Australia is depicted by light orange background with a minimum at
115 Ma.
S. Lavoué
Biogeography of the Asian and Australian arowanas
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Journal of Biogeography
S. Lavoué
Supporting Information
Biogeography of the Asian and Australian arowanas
9
Journal of Biogeography
Supporting Information
Figure S4 Bayesian time-calibrated phylogenetic trees under the O72R199 fossil
calibration strategies using the complete matrix 1 (panel A) and the matrix 1 that
excluded saturated partitions (panel B). Phylogenetic informativeness profiles of each
partition in each matrix are shown above to the corresponding tree. In both trees, the
age of the root is constraint to a minimum of 199.0 Ma while the age of the crown group
Osteoglossidae is constraint to a minimum of 72 Ma. Calibration constraints follow
exponential distributions. Elops hawaiensis is used to root the trees. Horizontal timescale is in millions of years ago (Ma). 95% age credibility intervals are shown as black
horizontal bars (focal node of interest), and grey horizontal bars (all other nodes). All
posterior probability support values at nodes equal 1 except for the Scleropages node in
reconstruction B which is equal to 0.96. The effective age prior on the age of Scleropages
is shown in (c), for each time-tree reconstruction. Timing of possible freshwater route
between Sundaland and Australia–New Guinea predating the separation between India
and Antarctica–Australia is depicted by light orange background with a minimum at
115 Ma.
S. Lavoué
Biogeography of the Asian and Australian arowanas
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Journal of Biogeography
S. Lavoué
Supporting Information
Biogeography of the Asian and Australian arowanas
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